Proof-of-concept sequence alignment algorithms library implemented in Impala.
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Prerequisites:
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a recent version of CMake (at least v3.7)
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for the CUDA benchmark an NVIDIA GPU with recent drivers and a working CUDA installation
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make sure, that the CUDA libraries are in your PATH before installing AnyDSL
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Install AnyDSL. In order to do so, run the "install_anydsl.sh" script provided. This will download, configure & compile AnyDSL which can take some time.
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After you have a working AnyDSL installation you can run the AnySeq build script:
./makeall.sh
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read sequences from files:
align [-o <output_file>] -i <FASTA file> <FASTA file> -
use random sequences:
align [-o <output_file>] -r [[<min length>] <max length>]